Starting phenix.real_space_refine on Sun Jul 5 15:23:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i8e_35249/07_2026/8i8e_35249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i8e_35249/07_2026/8i8e_35249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i8e_35249/07_2026/8i8e_35249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i8e_35249/07_2026/8i8e_35249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i8e_35249/07_2026/8i8e_35249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i8e_35249/07_2026/8i8e_35249.map" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 120 5.16 5 C 18564 2.51 5 N 4782 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29058 Number of models: 1 Model: "" Number of chains: 24 Chain: "f" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "D" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "b" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "c" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "d" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "e" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "f" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'AMP%rna3p': 1, 'OLA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'AMP%rna3p': 1, 'OLA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'AMP%rna3p': 1, 'OLA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'AMP%rna3p': 1, 'OLA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'AMP%rna3p': 1, 'OLA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'AMP%rna3p': 1, 'OLA': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "b" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "c" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "d" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "e" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 6.16, per 1000 atoms: 0.21 Number of scatterers: 29058 At special positions: 0 Unit cell: (189.618, 171.366, 92.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 12 15.00 O 5580 8.00 N 4782 7.00 C 18564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 30 sheets defined 40.7% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'f' and resid 2 through 15 removed outlier: 3.634A pdb=" N LYS f 8 " --> pdb=" O GLU f 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS f 9 " --> pdb=" O GLU f 5 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE f 11 " --> pdb=" O VAL f 7 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY f 12 " --> pdb=" O LYS f 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN f 14 " --> pdb=" O ILE f 10 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU f 15 " --> pdb=" O ILE f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 33 removed outlier: 3.747A pdb=" N LEU f 32 " --> pdb=" O VAL f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 51 removed outlier: 3.767A pdb=" N GLU f 47 " --> pdb=" O VAL f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 65 through 72 Processing helix chain 'D' and resid 14 through 21 removed outlier: 3.598A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 59 Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.648A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.505A pdb=" N GLY D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.799A pdb=" N GLN D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.927A pdb=" N THR D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 283 removed outlier: 3.733A pdb=" N LYS D 283 " --> pdb=" O PRO D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 283' Processing helix chain 'D' and resid 300 through 310 Processing helix chain 'D' and resid 321 through 324 removed outlier: 4.239A pdb=" N GLY D 324 " --> pdb=" O SER D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.612A pdb=" N GLU D 338 " --> pdb=" O GLU D 335 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 335 through 339' Processing helix chain 'D' and resid 340 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.579A pdb=" N TYR D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 483 through 493 Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.599A pdb=" N LEU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 59 Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.648A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 3.505A pdb=" N GLY A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.799A pdb=" N GLN A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 189 through 205 removed outlier: 3.927A pdb=" N THR A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.733A pdb=" N LYS A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 321 through 324 removed outlier: 4.239A pdb=" N GLY A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.612A pdb=" N GLU A 338 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 339' Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.579A pdb=" N TYR A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'F' and resid 14 through 21 removed outlier: 3.598A pdb=" N LEU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 59 Processing helix chain 'F' and resid 73 through 87 removed outlier: 3.648A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix removed outlier: 3.504A pdb=" N GLY F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.799A pdb=" N GLN F 126 " --> pdb=" O PRO F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 153 Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.927A pdb=" N THR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 231 through 240 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 283 removed outlier: 3.733A pdb=" N LYS F 283 " --> pdb=" O PRO F 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 283' Processing helix chain 'F' and resid 300 through 310 Processing helix chain 'F' and resid 321 through 324 removed outlier: 4.240A pdb=" N GLY F 324 " --> pdb=" O SER F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.612A pdb=" N GLU F 338 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 335 through 339' Processing helix chain 'F' and resid 340 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 removed outlier: 3.579A pdb=" N TYR F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 406' Processing helix chain 'F' and resid 440 through 449 Processing helix chain 'F' and resid 483 through 493 Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.598A pdb=" N LEU B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 59 Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.648A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 3.504A pdb=" N GLY B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.799A pdb=" N GLN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.927A pdb=" N THR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.734A pdb=" N LYS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 321 through 324 removed outlier: 4.240A pdb=" N GLY B 324 " --> pdb=" O SER B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.612A pdb=" N GLU B 338 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 335 through 339' Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.579A pdb=" N TYR B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'C' and resid 14 through 21 removed outlier: 3.597A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 59 Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.648A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 3.504A pdb=" N GLY C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.800A pdb=" N GLN C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.927A pdb=" N THR C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 283 removed outlier: 3.733A pdb=" N LYS C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 321 through 324 removed outlier: 4.240A pdb=" N GLY C 324 " --> pdb=" O SER C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.612A pdb=" N GLU C 338 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 339 " --> pdb=" O GLN C 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 335 through 339' Processing helix chain 'C' and resid 340 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.579A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 483 through 493 Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'E' and resid 14 through 21 removed outlier: 3.598A pdb=" N LEU E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 59 Processing helix chain 'E' and resid 73 through 87 removed outlier: 3.647A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix removed outlier: 3.505A pdb=" N GLY E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 120 through 126 removed outlier: 3.799A pdb=" N GLN E 126 " --> pdb=" O PRO E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'E' and resid 189 through 205 removed outlier: 3.927A pdb=" N THR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 283 removed outlier: 3.733A pdb=" N LYS E 283 " --> pdb=" O PRO E 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 300 through 310 Processing helix chain 'E' and resid 321 through 324 removed outlier: 4.240A pdb=" N GLY E 324 " --> pdb=" O SER E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.612A pdb=" N GLU E 338 " --> pdb=" O GLU E 335 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 339 " --> pdb=" O GLN E 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 335 through 339' Processing helix chain 'E' and resid 340 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 removed outlier: 3.579A pdb=" N TYR E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 440 through 449 Processing helix chain 'E' and resid 483 through 493 Processing helix chain 'E' and resid 524 through 533 Processing helix chain 'a' and resid 2 through 15 removed outlier: 3.634A pdb=" N LYS a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS a 9 " --> pdb=" O GLU a 5 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE a 11 " --> pdb=" O VAL a 7 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY a 12 " --> pdb=" O LYS a 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN a 14 " --> pdb=" O ILE a 10 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 33 removed outlier: 3.747A pdb=" N LEU a 32 " --> pdb=" O VAL a 29 " (cutoff:3.500A) Processing helix chain 'a' and resid 35 through 51 removed outlier: 3.767A pdb=" N GLU a 47 " --> pdb=" O VAL a 43 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 72 Processing helix chain 'b' and resid 2 through 15 removed outlier: 3.634A pdb=" N LYS b 8 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS b 9 " --> pdb=" O GLU b 5 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE b 11 " --> pdb=" O VAL b 7 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY b 12 " --> pdb=" O LYS b 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN b 14 " --> pdb=" O ILE b 10 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU b 15 " --> pdb=" O ILE b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 33 removed outlier: 3.747A pdb=" N LEU b 32 " --> pdb=" O VAL b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 35 through 51 removed outlier: 3.766A pdb=" N GLU b 47 " --> pdb=" O VAL b 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 65 through 72 Processing helix chain 'c' and resid 2 through 15 removed outlier: 3.634A pdb=" N LYS c 8 " --> pdb=" O GLU c 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS c 9 " --> pdb=" O GLU c 5 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE c 11 " --> pdb=" O VAL c 7 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY c 12 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN c 14 " --> pdb=" O ILE c 10 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU c 15 " --> pdb=" O ILE c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 29 through 33 removed outlier: 3.747A pdb=" N LEU c 32 " --> pdb=" O VAL c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 51 removed outlier: 3.766A pdb=" N GLU c 47 " --> pdb=" O VAL c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 65 through 72 Processing helix chain 'd' and resid 2 through 15 removed outlier: 3.634A pdb=" N LYS d 8 " --> pdb=" O GLU d 4 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS d 9 " --> pdb=" O GLU d 5 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE d 11 " --> pdb=" O VAL d 7 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN d 14 " --> pdb=" O ILE d 10 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU d 15 " --> pdb=" O ILE d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 33 removed outlier: 3.747A pdb=" N LEU d 32 " --> pdb=" O VAL d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 51 removed outlier: 3.767A pdb=" N GLU d 47 " --> pdb=" O VAL d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 72 Processing helix chain 'e' and resid 2 through 15 removed outlier: 3.634A pdb=" N LYS e 8 " --> pdb=" O GLU e 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS e 9 " --> pdb=" O GLU e 5 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE e 11 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN e 14 " --> pdb=" O ILE e 10 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU e 15 " --> pdb=" O ILE e 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 33 removed outlier: 3.747A pdb=" N LEU e 32 " --> pdb=" O VAL e 29 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 51 removed outlier: 3.767A pdb=" N GLU e 47 " --> pdb=" O VAL e 43 " (cutoff:3.500A) Processing helix chain 'e' and resid 65 through 72 Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.750A pdb=" N GLU D 30 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TYR D 245 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL D 32 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR D 218 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER D 266 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA D 316 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE D 329 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR D 318 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.577A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL D 66 " --> pdb=" O HIS D 91 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU D 90 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR D 174 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N MET D 92 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR D 172 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL D 185 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR D 174 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS D 183 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 359 through 363 removed outlier: 5.233A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 431 through 433 Processing sheet with id=AA5, first strand: chain 'D' and resid 456 through 461 removed outlier: 7.950A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.750A pdb=" N GLU A 30 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TYR A 245 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 32 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR A 218 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 266 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA A 316 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE A 329 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR A 318 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 140 removed outlier: 3.577A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 90 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR A 174 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N MET A 92 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR A 172 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 185 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A 174 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS A 183 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 363 removed outlier: 5.233A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AB1, first strand: chain 'A' and resid 456 through 461 removed outlier: 7.951A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.749A pdb=" N GLU F 30 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N TYR F 245 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL F 32 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR F 218 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER F 266 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA F 316 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE F 329 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR F 318 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.577A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL F 66 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU F 90 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR F 174 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N MET F 92 " --> pdb=" O TYR F 174 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR F 172 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL F 185 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR F 174 " --> pdb=" O LYS F 183 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS F 183 " --> pdb=" O TYR F 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 359 through 363 removed outlier: 5.232A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY F 410 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG F 426 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL F 412 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 431 through 433 Processing sheet with id=AB6, first strand: chain 'F' and resid 456 through 461 removed outlier: 7.951A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.750A pdb=" N GLU B 30 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TYR B 245 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 32 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR B 218 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 266 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA B 316 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE B 329 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR B 318 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 136 through 140 removed outlier: 3.577A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU B 90 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR B 174 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N MET B 92 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR B 172 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 185 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR B 174 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS B 183 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 359 through 363 removed outlier: 5.233A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 431 through 433 Processing sheet with id=AC2, first strand: chain 'B' and resid 456 through 461 removed outlier: 7.950A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.750A pdb=" N GLU C 30 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N TYR C 245 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C 32 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR C 218 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 266 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA C 316 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE C 329 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR C 318 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.576A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL C 66 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU C 90 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR C 174 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N MET C 92 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR C 172 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL C 185 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR C 174 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LYS C 183 " --> pdb=" O TYR C 174 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 359 through 363 removed outlier: 5.232A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 431 through 433 Processing sheet with id=AC7, first strand: chain 'C' and resid 456 through 461 removed outlier: 7.950A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.750A pdb=" N GLU E 30 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N TYR E 245 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL E 32 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR E 218 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER E 266 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA E 316 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE E 329 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR E 318 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.576A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL E 66 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU E 90 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR E 174 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N MET E 92 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR E 172 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 185 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR E 174 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LYS E 183 " --> pdb=" O TYR E 174 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 359 through 363 removed outlier: 5.233A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG E 426 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL E 412 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 431 through 433 Processing sheet with id=AD3, first strand: chain 'E' and resid 456 through 461 removed outlier: 7.950A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.24 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4992 1.31 - 1.44: 7392 1.44 - 1.56: 17028 1.56 - 1.69: 18 1.69 - 1.82: 216 Bond restraints: 29646 Sorted by residual: bond pdb=" C2' AMP A 701 " pdb=" C3' AMP A 701 " ideal model delta sigma weight residual 1.524 1.344 0.180 2.00e-02 2.50e+03 8.13e+01 bond pdb=" C2' AMP F 701 " pdb=" C3' AMP F 701 " ideal model delta sigma weight residual 1.524 1.344 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" C2' AMP B 701 " pdb=" C3' AMP B 701 " ideal model delta sigma weight residual 1.524 1.344 0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" C2' AMP C 701 " pdb=" C3' AMP C 701 " ideal model delta sigma weight residual 1.524 1.344 0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C2' AMP D 701 " pdb=" C3' AMP D 701 " ideal model delta sigma weight residual 1.524 1.345 0.179 2.00e-02 2.50e+03 8.05e+01 ... (remaining 29641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 39443 2.24 - 4.47: 603 4.47 - 6.71: 82 6.71 - 8.95: 24 8.95 - 11.19: 24 Bond angle restraints: 40176 Sorted by residual: angle pdb=" N GLN F 260 " pdb=" CA GLN F 260 " pdb=" C GLN F 260 " ideal model delta sigma weight residual 111.36 116.88 -5.52 1.09e+00 8.42e-01 2.56e+01 angle pdb=" N GLN A 260 " pdb=" CA GLN A 260 " pdb=" C GLN A 260 " ideal model delta sigma weight residual 111.36 116.86 -5.50 1.09e+00 8.42e-01 2.55e+01 angle pdb=" N GLN E 260 " pdb=" CA GLN E 260 " pdb=" C GLN E 260 " ideal model delta sigma weight residual 111.36 116.83 -5.47 1.09e+00 8.42e-01 2.52e+01 angle pdb=" N GLN D 260 " pdb=" CA GLN D 260 " pdb=" C GLN D 260 " ideal model delta sigma weight residual 111.36 116.83 -5.47 1.09e+00 8.42e-01 2.52e+01 angle pdb=" N GLN C 260 " pdb=" CA GLN C 260 " pdb=" C GLN C 260 " ideal model delta sigma weight residual 111.36 116.83 -5.47 1.09e+00 8.42e-01 2.52e+01 ... (remaining 40171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 15295 17.59 - 35.18: 1769 35.18 - 52.76: 579 52.76 - 70.35: 122 70.35 - 87.94: 43 Dihedral angle restraints: 17808 sinusoidal: 7278 harmonic: 10530 Sorted by residual: dihedral pdb=" C5' AMP A 701 " pdb=" O5' AMP A 701 " pdb=" P AMP A 701 " pdb=" O3P AMP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 11.97 -71.96 1 2.00e+01 2.50e-03 1.66e+01 dihedral pdb=" C5' AMP E 701 " pdb=" O5' AMP E 701 " pdb=" P AMP E 701 " pdb=" O3P AMP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 11.92 -71.92 1 2.00e+01 2.50e-03 1.66e+01 dihedral pdb=" C5' AMP C 701 " pdb=" O5' AMP C 701 " pdb=" P AMP C 701 " pdb=" O3P AMP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 11.89 -71.89 1 2.00e+01 2.50e-03 1.65e+01 ... (remaining 17805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2900 0.038 - 0.075: 1113 0.075 - 0.113: 443 0.113 - 0.151: 93 0.151 - 0.188: 23 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CA PRO B 223 " pdb=" N PRO B 223 " pdb=" C PRO B 223 " pdb=" CB PRO B 223 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CA PRO A 223 " pdb=" N PRO A 223 " pdb=" C PRO A 223 " pdb=" CB PRO A 223 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA PRO D 223 " pdb=" N PRO D 223 " pdb=" C PRO D 223 " pdb=" CB PRO D 223 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 4569 not shown) Planarity restraints: 5106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 333 " -0.055 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO E 334 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 334 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 334 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 333 " -0.055 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO C 334 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 334 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 334 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 333 " -0.055 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO A 334 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " -0.045 5.00e-02 4.00e+02 ... (remaining 5103 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3315 2.75 - 3.29: 27429 3.29 - 3.82: 48707 3.82 - 4.36: 61389 4.36 - 4.90: 100935 Nonbonded interactions: 241775 Sorted by model distance: nonbonded pdb=" O TYR B 41 " pdb=" ND1 HIS B 45 " model vdw 2.212 3.120 nonbonded pdb=" O TYR E 41 " pdb=" ND1 HIS E 45 " model vdw 2.213 3.120 nonbonded pdb=" O TYR D 41 " pdb=" ND1 HIS D 45 " model vdw 2.213 3.120 nonbonded pdb=" O TYR A 41 " pdb=" ND1 HIS A 45 " model vdw 2.213 3.120 nonbonded pdb=" O TYR C 41 " pdb=" ND1 HIS C 45 " model vdw 2.213 3.120 ... (remaining 241770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'f' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'D' selection = chain 'A' selection = chain 'F' selection = chain 'B' selection = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.430 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.198 29658 Z= 0.399 Angle : 0.747 11.185 40176 Z= 0.388 Chirality : 0.048 0.188 4572 Planarity : 0.006 0.082 5106 Dihedral : 17.482 87.941 11016 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.19 % Favored : 91.64 % Rotamer: Outliers : 0.76 % Allowed : 21.76 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3588 helix: 0.69 (0.15), residues: 1212 sheet: 0.18 (0.20), residues: 624 loop : -1.94 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.013 0.001 TYR A 245 PHE 0.013 0.002 PHE b 28 TRP 0.007 0.001 TRP E 230 HIS 0.007 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.37 (29646) covalent geometry : angle 0.74732 / 0.39 (40176) hydrogen bonds : bond 0.17895 / 11.74 ( 1032) hydrogen bonds : angle 6.75721 / 4.79 ( 2934) Misc. bond : bond 0.07278 / 5.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 MET cc_start: 0.8710 (mtp) cc_final: 0.8362 (mtp) REVERT: D 96 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7728 (mpt-90) REVERT: D 256 ASN cc_start: 0.8089 (t0) cc_final: 0.7740 (t0) REVERT: A 252 ASP cc_start: 0.7243 (m-30) cc_final: 0.7040 (m-30) REVERT: F 69 MET cc_start: 0.8723 (mtp) cc_final: 0.8191 (mtp) REVERT: F 96 ARG cc_start: 0.8080 (mmt90) cc_final: 0.7848 (mpt-90) REVERT: F 145 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7341 (tt0) REVERT: F 320 MET cc_start: 0.8919 (ptp) cc_final: 0.8661 (ptm) REVERT: F 331 GLN cc_start: 0.7873 (mm110) cc_final: 0.7579 (mm110) REVERT: F 461 MET cc_start: 0.1849 (OUTLIER) cc_final: 0.1361 (mpp) REVERT: C 7 ASP cc_start: 0.7063 (t0) cc_final: 0.6846 (t0) REVERT: C 69 MET cc_start: 0.8759 (mtp) cc_final: 0.8260 (mtp) REVERT: C 96 ARG cc_start: 0.8031 (mmt90) cc_final: 0.7791 (mpt-90) REVERT: C 125 ASP cc_start: 0.7439 (m-30) cc_final: 0.7160 (m-30) REVERT: C 145 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7260 (tt0) REVERT: C 320 MET cc_start: 0.8934 (ptp) cc_final: 0.8561 (ptp) REVERT: C 331 GLN cc_start: 0.7821 (mm110) cc_final: 0.7531 (mm110) REVERT: E 69 MET cc_start: 0.8689 (mtp) cc_final: 0.8348 (mtp) REVERT: E 256 ASN cc_start: 0.8140 (t0) cc_final: 0.7793 (t0) REVERT: E 396 LYS cc_start: 0.8517 (mttp) cc_final: 0.8285 (mttm) outliers start: 24 outliers final: 10 residues processed: 294 average time/residue: 0.7465 time to fit residues: 255.0596 Evaluate side-chains 246 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 235 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain c residue 69 ILE Chi-restraints excluded: chain d residue 69 ILE Chi-restraints excluded: chain e residue 69 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... f 19 GLN f 24 ASN D 154 GLN D 226 HIS A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 154 GLN E 226 HIS a 19 GLN a 24 ASN b 19 GLN b 24 ASN c 19 GLN c 24 ASN d 19 GLN d 24 ASN e 19 GLN e 24 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.194610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128421 restraints weight = 30677.564| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.91 r_work: 0.3156 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29658 Z= 0.133 Angle : 0.601 7.476 40176 Z= 0.309 Chirality : 0.046 0.173 4572 Planarity : 0.005 0.053 5106 Dihedral : 8.553 59.634 4067 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 3.44 % Allowed : 18.45 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3588 helix: 0.89 (0.15), residues: 1254 sheet: 0.04 (0.21), residues: 606 loop : -1.88 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 96 TYR 0.012 0.001 TYR E 245 PHE 0.014 0.001 PHE D 225 TRP 0.010 0.001 TRP F 437 HIS 0.005 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (29646) covalent geometry : angle 0.60109 / 0.31 (40176) hydrogen bonds : bond 0.04622 / 3.03 ( 1032) hydrogen bonds : angle 5.17761 / 3.68 ( 2934) Misc. bond : bond 0.00042 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 239 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 30 GLU cc_start: 0.2115 (mt-10) cc_final: 0.1557 (pt0) REVERT: f 58 GLU cc_start: 0.2462 (OUTLIER) cc_final: 0.0607 (tt0) REVERT: D 69 MET cc_start: 0.8877 (mtp) cc_final: 0.8560 (mtp) REVERT: D 96 ARG cc_start: 0.8426 (mmt90) cc_final: 0.8192 (mpt-90) REVERT: D 226 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6954 (m170) REVERT: D 256 ASN cc_start: 0.8379 (t0) cc_final: 0.8041 (t0) REVERT: A 62 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8099 (tmmt) REVERT: A 119 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: A 152 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8472 (tp) REVERT: A 256 ASN cc_start: 0.8506 (t0) cc_final: 0.7999 (t0) REVERT: A 461 MET cc_start: 0.1229 (mmm) cc_final: 0.0843 (mtt) REVERT: F 7 ASP cc_start: 0.7175 (t0) cc_final: 0.6962 (t0) REVERT: F 69 MET cc_start: 0.8909 (mtp) cc_final: 0.8527 (mtp) REVERT: F 96 ARG cc_start: 0.8548 (mmt90) cc_final: 0.8306 (mpt-90) REVERT: F 145 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7753 (tt0) REVERT: F 235 MET cc_start: 0.9112 (mtp) cc_final: 0.8788 (mtt) REVERT: F 320 MET cc_start: 0.8841 (ptp) cc_final: 0.8544 (ptm) REVERT: F 403 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7906 (ttp-110) REVERT: B 62 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8049 (tmmt) REVERT: B 125 ASP cc_start: 0.7659 (m-30) cc_final: 0.7355 (m-30) REVERT: B 152 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8430 (tp) REVERT: B 256 ASN cc_start: 0.8523 (t0) cc_final: 0.8042 (t0) REVERT: B 461 MET cc_start: 0.1090 (mmm) cc_final: 0.0689 (mtt) REVERT: C 69 MET cc_start: 0.8926 (mtp) cc_final: 0.8581 (mtp) REVERT: C 96 ARG cc_start: 0.8521 (mmt90) cc_final: 0.8320 (mpt-90) REVERT: C 125 ASP cc_start: 0.7746 (m-30) cc_final: 0.7538 (m-30) REVERT: C 145 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7697 (tt0) REVERT: C 226 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.7036 (m170) REVERT: C 235 MET cc_start: 0.9132 (mtp) cc_final: 0.8803 (mtt) REVERT: C 320 MET cc_start: 0.8854 (ptp) cc_final: 0.8552 (ptp) REVERT: E 226 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6983 (m170) REVERT: E 256 ASN cc_start: 0.8411 (t0) cc_final: 0.8033 (t0) outliers start: 108 outliers final: 44 residues processed: 335 average time/residue: 0.7659 time to fit residues: 297.2175 Evaluate side-chains 291 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 58 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 53 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 337 optimal weight: 40.0000 chunk 276 optimal weight: 0.9990 chunk 210 optimal weight: 5.9990 chunk 297 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 349 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 314 optimal weight: 0.9990 chunk 332 optimal weight: 30.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 GLN D 226 HIS A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 154 GLN E 226 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.193564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127153 restraints weight = 30670.579| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.86 r_work: 0.3136 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29658 Z= 0.149 Angle : 0.604 7.548 40176 Z= 0.311 Chirality : 0.047 0.183 4572 Planarity : 0.005 0.049 5106 Dihedral : 8.332 59.949 4056 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.22 % Favored : 92.50 % Rotamer: Outliers : 4.04 % Allowed : 17.78 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3588 helix: 0.99 (0.15), residues: 1248 sheet: -0.04 (0.22), residues: 534 loop : -1.74 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 403 TYR 0.014 0.001 TYR E 245 PHE 0.010 0.001 PHE C 173 TRP 0.007 0.001 TRP F 437 HIS 0.011 0.001 HIS E 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (29646) covalent geometry : angle 0.60446 / 0.31 (40176) hydrogen bonds : bond 0.04556 / 3.00 ( 1032) hydrogen bonds : angle 4.93478 / 3.50 ( 2934) Misc. bond : bond 0.00035 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 232 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 58 GLU cc_start: 0.2453 (OUTLIER) cc_final: 0.0633 (tt0) REVERT: D 62 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7991 (tmtt) REVERT: D 69 MET cc_start: 0.8906 (mtp) cc_final: 0.8597 (mtp) REVERT: D 96 ARG cc_start: 0.8428 (mmt90) cc_final: 0.8180 (mpt-90) REVERT: D 232 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8806 (mm) REVERT: D 252 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: D 256 ASN cc_start: 0.8416 (t0) cc_final: 0.8090 (t0) REVERT: D 331 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7088 (mt0) REVERT: A 62 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8087 (tmmt) REVERT: A 119 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: A 158 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: A 252 ASP cc_start: 0.7910 (m-30) cc_final: 0.7679 (m-30) REVERT: A 256 ASN cc_start: 0.8516 (t0) cc_final: 0.8021 (t0) REVERT: A 365 GLU cc_start: 0.7933 (mp0) cc_final: 0.7720 (mp0) REVERT: F 7 ASP cc_start: 0.7176 (t0) cc_final: 0.6960 (t0) REVERT: F 62 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7320 (ttpt) REVERT: F 69 MET cc_start: 0.8954 (mtp) cc_final: 0.8590 (mtp) REVERT: F 96 ARG cc_start: 0.8571 (mmt90) cc_final: 0.8348 (mpt-90) REVERT: F 145 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7749 (tt0) REVERT: F 320 MET cc_start: 0.8861 (ptp) cc_final: 0.8591 (ptm) REVERT: F 331 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.6928 (mt0) REVERT: F 461 MET cc_start: 0.2376 (mmm) cc_final: 0.2053 (mpp) REVERT: B 62 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8047 (tmmt) REVERT: B 152 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8353 (tp) REVERT: B 256 ASN cc_start: 0.8520 (t0) cc_final: 0.8054 (t0) REVERT: B 346 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: B 461 MET cc_start: 0.1026 (mmm) cc_final: 0.0606 (mtt) REVERT: C 7 ASP cc_start: 0.7045 (t0) cc_final: 0.6802 (t0) REVERT: C 62 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7379 (ttpt) REVERT: C 69 MET cc_start: 0.8974 (mtp) cc_final: 0.8624 (mtp) REVERT: C 96 ARG cc_start: 0.8561 (mmt90) cc_final: 0.8350 (mpt-90) REVERT: C 125 ASP cc_start: 0.7798 (m-30) cc_final: 0.7585 (m-30) REVERT: C 145 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7694 (tt0) REVERT: C 320 MET cc_start: 0.8872 (ptp) cc_final: 0.8590 (ptm) REVERT: C 331 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.6970 (mt0) REVERT: E 226 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.7149 (m170) REVERT: E 232 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8804 (mm) REVERT: E 252 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: E 256 ASN cc_start: 0.8473 (t0) cc_final: 0.8118 (t0) REVERT: E 461 MET cc_start: 0.0423 (mtt) cc_final: -0.0441 (mmm) outliers start: 127 outliers final: 69 residues processed: 338 average time/residue: 0.7494 time to fit residues: 294.3308 Evaluate side-chains 312 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 225 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 58 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 113 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 273 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 170 optimal weight: 0.9990 chunk 258 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 GLN D 226 HIS D 390 ASN A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 226 HIS E 390 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.192172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125699 restraints weight = 30531.688| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.94 r_work: 0.3105 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29658 Z= 0.189 Angle : 0.641 7.758 40176 Z= 0.331 Chirality : 0.048 0.201 4572 Planarity : 0.005 0.048 5106 Dihedral : 8.346 59.994 4056 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.47 % Favored : 92.20 % Rotamer: Outliers : 4.39 % Allowed : 17.65 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3588 helix: 0.85 (0.15), residues: 1266 sheet: -0.27 (0.20), residues: 618 loop : -1.82 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 403 TYR 0.018 0.002 TYR E 245 PHE 0.015 0.002 PHE D 225 TRP 0.010 0.001 TRP A 290 HIS 0.025 0.002 HIS E 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (29646) covalent geometry : angle 0.64059 / 0.33 (40176) hydrogen bonds : bond 0.04847 / 3.20 ( 1032) hydrogen bonds : angle 4.88431 / 3.46 ( 2934) Misc. bond : bond 0.00032 / 0.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 233 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 58 GLU cc_start: 0.2386 (OUTLIER) cc_final: 0.0638 (tt0) REVERT: D 62 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8031 (tmtt) REVERT: D 69 MET cc_start: 0.8893 (mtp) cc_final: 0.8596 (mtp) REVERT: D 232 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8831 (mm) REVERT: D 252 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: D 256 ASN cc_start: 0.8427 (t0) cc_final: 0.8116 (t0) REVERT: D 331 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7202 (mt0) REVERT: A 31 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8745 (mm) REVERT: A 119 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8407 (mt-10) REVERT: A 158 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: A 252 ASP cc_start: 0.8009 (m-30) cc_final: 0.7748 (m-30) REVERT: A 256 ASN cc_start: 0.8489 (t0) cc_final: 0.7991 (t0) REVERT: A 461 MET cc_start: 0.1302 (mmm) cc_final: 0.0798 (mtt) REVERT: F 7 ASP cc_start: 0.7306 (t0) cc_final: 0.7037 (t0) REVERT: F 62 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7301 (ttpt) REVERT: F 69 MET cc_start: 0.8962 (mtp) cc_final: 0.8571 (mtp) REVERT: F 96 ARG cc_start: 0.8608 (mmt90) cc_final: 0.8363 (mpt-90) REVERT: F 145 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7695 (tt0) REVERT: F 320 MET cc_start: 0.8889 (ptp) cc_final: 0.8631 (ptm) REVERT: F 331 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7149 (mt0) REVERT: B 31 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8766 (mm) REVERT: B 62 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7979 (tmmt) REVERT: B 125 ASP cc_start: 0.7615 (m-30) cc_final: 0.7339 (m-30) REVERT: B 256 ASN cc_start: 0.8523 (t0) cc_final: 0.8050 (t0) REVERT: B 365 GLU cc_start: 0.7926 (mp0) cc_final: 0.7699 (mp0) REVERT: B 461 MET cc_start: 0.1113 (mmm) cc_final: 0.0660 (mtt) REVERT: C 7 ASP cc_start: 0.7242 (t0) cc_final: 0.6951 (t0) REVERT: C 69 MET cc_start: 0.8968 (mtp) cc_final: 0.8567 (mtp) REVERT: C 96 ARG cc_start: 0.8567 (mmt90) cc_final: 0.8298 (mpt-90) REVERT: C 125 ASP cc_start: 0.7862 (m-30) cc_final: 0.7643 (m-30) REVERT: C 145 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7649 (tt0) REVERT: C 226 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.6995 (m170) REVERT: C 320 MET cc_start: 0.8904 (ptp) cc_final: 0.8607 (ptm) REVERT: C 331 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: C 461 MET cc_start: 0.0562 (mtt) cc_final: 0.0256 (mpp) REVERT: E 232 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8833 (mm) REVERT: E 252 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: E 256 ASN cc_start: 0.8476 (t0) cc_final: 0.8135 (t0) REVERT: E 331 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7183 (mt0) REVERT: E 461 MET cc_start: 0.0625 (mtt) cc_final: -0.0226 (mmm) REVERT: e 30 GLU cc_start: 0.2743 (OUTLIER) cc_final: 0.2200 (tm-30) outliers start: 138 outliers final: 75 residues processed: 343 average time/residue: 0.6953 time to fit residues: 279.6392 Evaluate side-chains 330 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 237 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 58 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 39 THR Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 210 optimal weight: 0.5980 chunk 277 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 342 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 130 optimal weight: 0.0570 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 GLN D 226 HIS D 532 HIS A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 226 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.194541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127705 restraints weight = 30666.379| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.82 r_work: 0.3158 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29658 Z= 0.116 Angle : 0.569 7.334 40176 Z= 0.291 Chirality : 0.045 0.164 4572 Planarity : 0.004 0.045 5106 Dihedral : 7.908 59.994 4055 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.35 % Favored : 93.31 % Rotamer: Outliers : 3.56 % Allowed : 19.15 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3588 helix: 1.17 (0.15), residues: 1266 sheet: -0.15 (0.22), residues: 540 loop : -1.65 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.009 0.001 TYR B 245 PHE 0.011 0.001 PHE D 225 TRP 0.007 0.001 TRP C 290 HIS 0.022 0.001 HIS C 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (29646) covalent geometry : angle 0.56941 / 0.29 (40176) hydrogen bonds : bond 0.03788 / 2.49 ( 1032) hydrogen bonds : angle 4.64053 / 3.28 ( 2934) Misc. bond : bond 0.00030 / 0.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 245 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 58 GLU cc_start: 0.2190 (OUTLIER) cc_final: 0.0646 (tt0) REVERT: D 62 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7956 (tmtt) REVERT: D 69 MET cc_start: 0.8839 (mtp) cc_final: 0.8573 (mtp) REVERT: D 252 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: D 256 ASN cc_start: 0.8385 (t0) cc_final: 0.8069 (t0) REVERT: D 468 GLU cc_start: 0.5041 (OUTLIER) cc_final: 0.3959 (mm-30) REVERT: A 112 ASP cc_start: 0.8666 (m-30) cc_final: 0.8437 (m-30) REVERT: A 119 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8350 (mt-10) REVERT: A 152 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 256 ASN cc_start: 0.8490 (t0) cc_final: 0.8015 (t0) REVERT: A 461 MET cc_start: 0.1327 (mmm) cc_final: 0.0829 (mtt) REVERT: F 7 ASP cc_start: 0.7146 (t0) cc_final: 0.6888 (t0) REVERT: F 69 MET cc_start: 0.8888 (mtp) cc_final: 0.8526 (mtp) REVERT: F 96 ARG cc_start: 0.8570 (mmt90) cc_final: 0.8317 (mpt-90) REVERT: F 145 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7713 (tt0) REVERT: F 320 MET cc_start: 0.8801 (ptp) cc_final: 0.8564 (ptm) REVERT: F 331 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6971 (mt0) REVERT: B 62 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.8020 (tmmt) REVERT: B 152 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8387 (tp) REVERT: B 256 ASN cc_start: 0.8491 (t0) cc_final: 0.8053 (t0) REVERT: B 346 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: B 461 MET cc_start: 0.1126 (mmm) cc_final: 0.0775 (mtt) REVERT: C 7 ASP cc_start: 0.7120 (t0) cc_final: 0.6809 (t0) REVERT: C 69 MET cc_start: 0.8920 (mtp) cc_final: 0.8568 (mtp) REVERT: C 96 ARG cc_start: 0.8552 (mmt90) cc_final: 0.8298 (mpt-90) REVERT: C 125 ASP cc_start: 0.7805 (m-30) cc_final: 0.7493 (m-30) REVERT: C 145 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7658 (tt0) REVERT: C 320 MET cc_start: 0.8842 (ptp) cc_final: 0.8580 (ptm) REVERT: C 331 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.6972 (mt0) REVERT: E 252 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: E 256 ASN cc_start: 0.8412 (t0) cc_final: 0.8074 (t0) REVERT: E 461 MET cc_start: 0.0603 (mtt) cc_final: -0.0019 (mmm) REVERT: a 57 GLU cc_start: 0.3792 (mm-30) cc_final: 0.3385 (mp0) REVERT: e 30 GLU cc_start: 0.2655 (OUTLIER) cc_final: 0.2163 (tm-30) outliers start: 112 outliers final: 59 residues processed: 337 average time/residue: 0.7083 time to fit residues: 279.4730 Evaluate side-chains 306 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 234 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 58 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 91 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 326 optimal weight: 30.0000 chunk 134 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 352 optimal weight: 30.0000 chunk 249 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 GLN D 226 HIS D 532 HIS A 154 GLN A 226 HIS F 154 GLN B 154 GLN B 226 HIS C 226 HIS E 226 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.194643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127762 restraints weight = 30432.855| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.80 r_work: 0.3161 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29658 Z= 0.116 Angle : 0.572 9.210 40176 Z= 0.290 Chirality : 0.045 0.163 4572 Planarity : 0.004 0.044 5106 Dihedral : 7.712 59.922 4055 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.44 % Favored : 93.20 % Rotamer: Outliers : 3.50 % Allowed : 19.97 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3588 helix: 1.27 (0.15), residues: 1272 sheet: -0.12 (0.22), residues: 540 loop : -1.61 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 96 TYR 0.010 0.001 TYR F 245 PHE 0.011 0.001 PHE D 225 TRP 0.006 0.001 TRP B 230 HIS 0.009 0.001 HIS E 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (29646) covalent geometry : angle 0.57204 / 0.29 (40176) hydrogen bonds : bond 0.03721 / 2.45 ( 1032) hydrogen bonds : angle 4.55168 / 3.21 ( 2934) Misc. bond : bond 0.00018 / 0.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 243 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7970 (tmtt) REVERT: D 69 MET cc_start: 0.8852 (mtp) cc_final: 0.8569 (mtp) REVERT: D 86 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8448 (mp) REVERT: D 252 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7240 (m-30) REVERT: D 256 ASN cc_start: 0.8373 (t0) cc_final: 0.8054 (t0) REVERT: D 338 GLU cc_start: 0.8194 (mp0) cc_final: 0.7835 (mp0) REVERT: D 468 GLU cc_start: 0.4949 (OUTLIER) cc_final: 0.3841 (mm-30) REVERT: A 112 ASP cc_start: 0.8661 (m-30) cc_final: 0.8431 (m-30) REVERT: A 119 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: A 152 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8301 (tp) REVERT: A 256 ASN cc_start: 0.8483 (t0) cc_final: 0.8006 (t0) REVERT: A 461 MET cc_start: 0.1419 (mmm) cc_final: 0.0965 (mtt) REVERT: F 7 ASP cc_start: 0.7125 (t0) cc_final: 0.6857 (t0) REVERT: F 62 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7297 (ttpt) REVERT: F 69 MET cc_start: 0.8876 (mtp) cc_final: 0.8506 (mtp) REVERT: F 96 ARG cc_start: 0.8560 (mmt90) cc_final: 0.8315 (mpt-90) REVERT: F 145 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7692 (tt0) REVERT: F 235 MET cc_start: 0.9105 (mtp) cc_final: 0.8845 (mtt) REVERT: F 320 MET cc_start: 0.8802 (ptp) cc_final: 0.8551 (ptm) REVERT: F 331 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7058 (mt0) REVERT: B 62 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.8010 (tmmt) REVERT: B 152 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8383 (tp) REVERT: B 256 ASN cc_start: 0.8487 (t0) cc_final: 0.8038 (t0) REVERT: B 283 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7913 (mmmm) REVERT: B 365 GLU cc_start: 0.7928 (mp0) cc_final: 0.7721 (mp0) REVERT: B 461 MET cc_start: 0.1320 (mmm) cc_final: 0.0815 (mtt) REVERT: C 7 ASP cc_start: 0.7095 (t0) cc_final: 0.6772 (t0) REVERT: C 62 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7301 (ttpt) REVERT: C 69 MET cc_start: 0.8917 (mtp) cc_final: 0.8567 (mtp) REVERT: C 96 ARG cc_start: 0.8556 (mmt90) cc_final: 0.8301 (mpt-90) REVERT: C 125 ASP cc_start: 0.7784 (m-30) cc_final: 0.7459 (m-30) REVERT: C 145 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7623 (tt0) REVERT: C 320 MET cc_start: 0.8828 (ptp) cc_final: 0.8549 (ptm) REVERT: C 331 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.6943 (mt0) REVERT: E 69 MET cc_start: 0.8993 (mtm) cc_final: 0.8609 (mtp) REVERT: E 86 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8429 (mp) REVERT: E 252 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: E 256 ASN cc_start: 0.8386 (t0) cc_final: 0.8044 (t0) REVERT: a 30 GLU cc_start: 0.2417 (OUTLIER) cc_final: 0.1617 (pt0) REVERT: e 30 GLU cc_start: 0.2510 (OUTLIER) cc_final: 0.2019 (tm-30) outliers start: 110 outliers final: 61 residues processed: 336 average time/residue: 0.7373 time to fit residues: 288.5972 Evaluate side-chains 317 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 240 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 30 GLU Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 291 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 chunk 352 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 125 optimal weight: 0.0370 chunk 264 optimal weight: 0.8980 overall best weight: 1.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 GLN D 226 HIS A 154 GLN A 226 HIS F 154 GLN B 154 GLN B 226 HIS E 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.192916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125895 restraints weight = 30561.390| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.81 r_work: 0.3136 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29658 Z= 0.165 Angle : 0.617 8.243 40176 Z= 0.315 Chirality : 0.047 0.187 4572 Planarity : 0.004 0.045 5106 Dihedral : 7.915 59.966 4055 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.08 % Favored : 92.56 % Rotamer: Outliers : 3.56 % Allowed : 20.45 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3588 helix: 1.15 (0.15), residues: 1266 sheet: -0.23 (0.20), residues: 618 loop : -1.79 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.015 0.002 TYR E 245 PHE 0.015 0.002 PHE E 225 TRP 0.010 0.001 TRP D 290 HIS 0.008 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 (29646) covalent geometry : angle 0.61730 / 0.32 (40176) hydrogen bonds : bond 0.04386 / 2.90 ( 1032) hydrogen bonds : angle 4.66874 / 3.29 ( 2934) Misc. bond : bond 0.00015 / 0.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 238 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 30 GLU cc_start: 0.2392 (OUTLIER) cc_final: 0.2164 (tt0) REVERT: D 31 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8447 (mm) REVERT: D 62 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7964 (tmtt) REVERT: D 69 MET cc_start: 0.8879 (mtp) cc_final: 0.8588 (mtp) REVERT: D 158 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: D 232 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8798 (mm) REVERT: D 252 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7280 (m-30) REVERT: D 256 ASN cc_start: 0.8391 (t0) cc_final: 0.8091 (t0) REVERT: D 337 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8224 (mm) REVERT: D 338 GLU cc_start: 0.8258 (mp0) cc_final: 0.7954 (mp0) REVERT: A 112 ASP cc_start: 0.8657 (m-30) cc_final: 0.8434 (m-30) REVERT: A 119 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8363 (mt-10) REVERT: A 152 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8299 (tp) REVERT: A 252 ASP cc_start: 0.7942 (m-30) cc_final: 0.7706 (m-30) REVERT: A 256 ASN cc_start: 0.8489 (t0) cc_final: 0.8015 (t0) REVERT: A 461 MET cc_start: 0.1527 (mmm) cc_final: 0.1027 (mtt) REVERT: F 7 ASP cc_start: 0.7197 (t0) cc_final: 0.6906 (t0) REVERT: F 62 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7247 (ttpt) REVERT: F 69 MET cc_start: 0.8915 (mtp) cc_final: 0.8503 (mtp) REVERT: F 96 ARG cc_start: 0.8590 (mmt90) cc_final: 0.8339 (mpt-90) REVERT: F 145 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7696 (tt0) REVERT: F 320 MET cc_start: 0.8858 (ptp) cc_final: 0.8610 (ptm) REVERT: B 31 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8717 (mm) REVERT: B 62 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7997 (tmmt) REVERT: B 125 ASP cc_start: 0.7696 (m-30) cc_final: 0.7410 (m-30) REVERT: B 256 ASN cc_start: 0.8520 (t0) cc_final: 0.8068 (t0) REVERT: B 283 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7953 (mmmm) REVERT: C 7 ASP cc_start: 0.7155 (t0) cc_final: 0.6826 (t0) REVERT: C 69 MET cc_start: 0.8938 (mtp) cc_final: 0.8555 (mtp) REVERT: C 96 ARG cc_start: 0.8576 (mmt90) cc_final: 0.8309 (mpt-90) REVERT: C 125 ASP cc_start: 0.7810 (m-30) cc_final: 0.7480 (m-30) REVERT: C 145 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7635 (tt0) REVERT: C 320 MET cc_start: 0.8862 (ptp) cc_final: 0.8558 (ptm) REVERT: C 331 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7021 (mt0) REVERT: E 31 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8460 (mm) REVERT: E 232 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8806 (mm) REVERT: E 252 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: E 256 ASN cc_start: 0.8426 (t0) cc_final: 0.8085 (t0) REVERT: E 337 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8333 (mm) REVERT: E 346 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: a 5 GLU cc_start: 0.3568 (OUTLIER) cc_final: 0.3226 (mm-30) REVERT: a 30 GLU cc_start: 0.2610 (OUTLIER) cc_final: 0.1778 (pt0) REVERT: e 30 GLU cc_start: 0.2849 (OUTLIER) cc_final: 0.2221 (tm-30) outliers start: 112 outliers final: 67 residues processed: 331 average time/residue: 0.7133 time to fit residues: 275.3634 Evaluate side-chains 324 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 236 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 30 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 468 GLU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 346 GLU Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 30 GLU Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 282 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 chunk 312 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 254 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 GLN D 226 HIS A 154 GLN A 226 HIS F 154 GLN B 154 GLN B 226 HIS E 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.193710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127713 restraints weight = 30598.744| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.31 r_work: 0.3140 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29658 Z= 0.140 Angle : 0.595 8.081 40176 Z= 0.302 Chirality : 0.046 0.176 4572 Planarity : 0.004 0.045 5106 Dihedral : 7.798 59.971 4053 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.72 % Favored : 92.89 % Rotamer: Outliers : 3.37 % Allowed : 20.74 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3588 helix: 1.20 (0.15), residues: 1272 sheet: -0.18 (0.22), residues: 540 loop : -1.68 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.012 0.001 TYR C 245 PHE 0.012 0.001 PHE E 225 TRP 0.007 0.001 TRP B 230 HIS 0.007 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (29646) covalent geometry : angle 0.59490 / 0.30 (40176) hydrogen bonds : bond 0.04029 / 2.66 ( 1032) hydrogen bonds : angle 4.59250 / 3.24 ( 2934) Misc. bond : bond 0.00020 / 0.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 234 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8444 (mm) REVERT: D 62 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7947 (tmtt) REVERT: D 69 MET cc_start: 0.8854 (mtp) cc_final: 0.8559 (mtp) REVERT: D 158 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: D 252 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: D 256 ASN cc_start: 0.8380 (t0) cc_final: 0.8064 (t0) REVERT: D 337 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8250 (mm) REVERT: D 468 GLU cc_start: 0.5026 (OUTLIER) cc_final: 0.3846 (mm-30) REVERT: D 473 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5414 (tp) REVERT: A 31 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8692 (mm) REVERT: A 112 ASP cc_start: 0.8673 (m-30) cc_final: 0.8457 (m-30) REVERT: A 119 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: A 152 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 256 ASN cc_start: 0.8526 (t0) cc_final: 0.8053 (t0) REVERT: A 461 MET cc_start: 0.1526 (mmm) cc_final: 0.1010 (mtt) REVERT: F 7 ASP cc_start: 0.7168 (t0) cc_final: 0.6868 (t0) REVERT: F 62 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7242 (ttpt) REVERT: F 69 MET cc_start: 0.8889 (mtp) cc_final: 0.8488 (mtp) REVERT: F 96 ARG cc_start: 0.8594 (mmt90) cc_final: 0.8357 (mpt-90) REVERT: F 145 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7720 (tt0) REVERT: F 320 MET cc_start: 0.8845 (ptp) cc_final: 0.8607 (ptm) REVERT: B 62 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.8010 (tmmt) REVERT: B 152 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8334 (tp) REVERT: B 256 ASN cc_start: 0.8507 (t0) cc_final: 0.8057 (t0) REVERT: B 283 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7942 (mmmm) REVERT: B 461 MET cc_start: 0.1486 (mmm) cc_final: 0.1108 (mtt) REVERT: C 7 ASP cc_start: 0.7121 (t0) cc_final: 0.6781 (t0) REVERT: C 69 MET cc_start: 0.8944 (mtp) cc_final: 0.8565 (mtp) REVERT: C 96 ARG cc_start: 0.8578 (mmt90) cc_final: 0.8313 (mpt-90) REVERT: C 125 ASP cc_start: 0.7869 (m-30) cc_final: 0.7548 (m-30) REVERT: C 145 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7657 (tt0) REVERT: C 224 MET cc_start: 0.8410 (ttt) cc_final: 0.8008 (ttt) REVERT: C 320 MET cc_start: 0.8853 (ptp) cc_final: 0.8560 (ptm) REVERT: C 331 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7014 (mt0) REVERT: E 31 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8461 (mm) REVERT: E 232 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8784 (mm) REVERT: E 252 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: E 256 ASN cc_start: 0.8420 (t0) cc_final: 0.8063 (t0) REVERT: E 337 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8292 (mm) REVERT: E 461 MET cc_start: -0.0221 (mpt) cc_final: -0.0509 (ttm) REVERT: a 5 GLU cc_start: 0.3545 (OUTLIER) cc_final: 0.3202 (mm-30) REVERT: a 30 GLU cc_start: 0.2454 (OUTLIER) cc_final: 0.1762 (pt0) REVERT: e 30 GLU cc_start: 0.2813 (OUTLIER) cc_final: 0.2199 (tm-30) outliers start: 106 outliers final: 65 residues processed: 325 average time/residue: 0.7231 time to fit residues: 274.3071 Evaluate side-chains 320 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 234 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 30 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain F residue 468 GLU Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 30 GLU Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 325 optimal weight: 40.0000 chunk 253 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 352 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 GLN D 226 HIS A 154 GLN A 226 HIS F 154 GLN B 154 GLN B 226 HIS E 226 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.195950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129400 restraints weight = 30451.739| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.30 r_work: 0.3138 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29658 Z= 0.123 Angle : 0.583 8.263 40176 Z= 0.295 Chirality : 0.046 0.166 4572 Planarity : 0.004 0.044 5106 Dihedral : 7.620 60.000 4053 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.61 % Favored : 93.00 % Rotamer: Outliers : 3.40 % Allowed : 20.67 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3588 helix: 1.32 (0.15), residues: 1242 sheet: -0.14 (0.22), residues: 540 loop : -1.64 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.011 0.001 TYR B 245 PHE 0.011 0.001 PHE D 225 TRP 0.008 0.001 TRP B 230 HIS 0.007 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (29646) covalent geometry : angle 0.58316 / 0.30 (40176) hydrogen bonds : bond 0.03769 / 2.48 ( 1032) hydrogen bonds : angle 4.51702 / 3.18 ( 2934) Misc. bond : bond 0.00019 / 0.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 236 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 ASP cc_start: 0.6881 (t0) cc_final: 0.6659 (t0) REVERT: D 62 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7944 (tmtt) REVERT: D 69 MET cc_start: 0.8861 (mtp) cc_final: 0.8562 (mtp) REVERT: D 158 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: D 252 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: D 256 ASN cc_start: 0.8374 (t0) cc_final: 0.8063 (t0) REVERT: D 331 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7181 (mt0) REVERT: D 337 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8256 (mm) REVERT: D 468 GLU cc_start: 0.4934 (OUTLIER) cc_final: 0.3821 (mm-30) REVERT: D 473 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5402 (tp) REVERT: A 31 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8670 (mm) REVERT: A 119 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8405 (mt-10) REVERT: A 152 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8290 (tp) REVERT: A 256 ASN cc_start: 0.8507 (t0) cc_final: 0.8044 (t0) REVERT: A 461 MET cc_start: 0.1320 (mmm) cc_final: 0.0985 (mtt) REVERT: F 7 ASP cc_start: 0.7153 (t0) cc_final: 0.6848 (t0) REVERT: F 62 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7322 (ttpt) REVERT: F 69 MET cc_start: 0.8906 (mtp) cc_final: 0.8536 (mtp) REVERT: F 96 ARG cc_start: 0.8578 (mmt90) cc_final: 0.8308 (mpt-90) REVERT: F 145 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7728 (tt0) REVERT: F 320 MET cc_start: 0.8839 (ptp) cc_final: 0.8600 (ptm) REVERT: B 31 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8710 (mm) REVERT: B 62 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.8020 (tmmt) REVERT: B 152 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8297 (tp) REVERT: B 256 ASN cc_start: 0.8520 (t0) cc_final: 0.8066 (t0) REVERT: B 283 LYS cc_start: 0.8337 (mmtt) cc_final: 0.7896 (mmmm) REVERT: B 365 GLU cc_start: 0.7882 (mp0) cc_final: 0.7676 (mp0) REVERT: C 7 ASP cc_start: 0.7097 (t0) cc_final: 0.6744 (t0) REVERT: C 69 MET cc_start: 0.8939 (mtp) cc_final: 0.8587 (mtp) REVERT: C 96 ARG cc_start: 0.8585 (mmt90) cc_final: 0.8342 (mpt-90) REVERT: C 125 ASP cc_start: 0.7868 (m-30) cc_final: 0.7554 (m-30) REVERT: C 145 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7639 (tt0) REVERT: C 224 MET cc_start: 0.8421 (ttt) cc_final: 0.7987 (ttt) REVERT: C 320 MET cc_start: 0.8857 (ptp) cc_final: 0.8494 (ptp) REVERT: C 331 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7004 (mt0) REVERT: E 232 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8753 (mm) REVERT: E 252 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: E 256 ASN cc_start: 0.8409 (t0) cc_final: 0.8062 (t0) REVERT: E 337 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8284 (mm) REVERT: E 461 MET cc_start: 0.0103 (mpt) cc_final: -0.0156 (ttm) REVERT: e 30 GLU cc_start: 0.2705 (OUTLIER) cc_final: 0.2126 (tm-30) outliers start: 107 outliers final: 66 residues processed: 329 average time/residue: 0.7288 time to fit residues: 279.6752 Evaluate side-chains 317 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 232 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 30 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 468 GLU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 327 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 255 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 280 optimal weight: 0.6980 chunk 145 optimal weight: 0.0570 chunk 114 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 GLN D 226 HIS A 154 GLN A 226 HIS F 154 GLN B 154 GLN B 226 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.195833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129588 restraints weight = 30346.300| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.79 r_work: 0.3187 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29658 Z= 0.104 Angle : 0.571 8.683 40176 Z= 0.287 Chirality : 0.045 0.155 4572 Planarity : 0.004 0.044 5106 Dihedral : 7.420 59.839 4053 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.13 % Favored : 93.48 % Rotamer: Outliers : 2.45 % Allowed : 21.60 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3588 helix: 1.40 (0.15), residues: 1254 sheet: -0.13 (0.23), residues: 540 loop : -1.54 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.008 0.001 TYR C 148 PHE 0.010 0.001 PHE E 225 TRP 0.009 0.001 TRP A 290 HIS 0.006 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (29646) covalent geometry : angle 0.57091 / 0.29 (40176) hydrogen bonds : bond 0.03360 / 2.21 ( 1032) hydrogen bonds : angle 4.41714 / 3.11 ( 2934) Misc. bond : bond 0.00018 / 0.01 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 239 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7927 (tmtt) REVERT: D 69 MET cc_start: 0.8822 (mtp) cc_final: 0.8552 (mtp) REVERT: D 252 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: D 256 ASN cc_start: 0.8307 (t0) cc_final: 0.7995 (t0) REVERT: D 461 MET cc_start: 0.0387 (mpp) cc_final: -0.0148 (ttm) REVERT: D 468 GLU cc_start: 0.4961 (OUTLIER) cc_final: 0.3829 (mm-30) REVERT: A 31 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8661 (mm) REVERT: A 152 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 256 ASN cc_start: 0.8457 (t0) cc_final: 0.7994 (t0) REVERT: A 461 MET cc_start: 0.1340 (mmm) cc_final: 0.0902 (mtt) REVERT: F 7 ASP cc_start: 0.7075 (t0) cc_final: 0.6792 (t0) REVERT: F 62 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7175 (ttpt) REVERT: F 69 MET cc_start: 0.8876 (mtp) cc_final: 0.8529 (mtp) REVERT: F 96 ARG cc_start: 0.8561 (mmt90) cc_final: 0.8313 (mpt-90) REVERT: F 145 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7701 (tt0) REVERT: F 235 MET cc_start: 0.9084 (mtp) cc_final: 0.8789 (mtt) REVERT: F 320 MET cc_start: 0.8813 (ptp) cc_final: 0.8571 (ptm) REVERT: B 31 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8699 (mm) REVERT: B 152 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8345 (tp) REVERT: B 256 ASN cc_start: 0.8476 (t0) cc_final: 0.8032 (t0) REVERT: B 283 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7914 (mmmm) REVERT: B 365 GLU cc_start: 0.7871 (mp0) cc_final: 0.7625 (mp0) REVERT: C 7 ASP cc_start: 0.7044 (t0) cc_final: 0.6706 (t0) REVERT: C 69 MET cc_start: 0.8910 (mtp) cc_final: 0.8580 (mtp) REVERT: C 96 ARG cc_start: 0.8562 (mmt90) cc_final: 0.8338 (mpt-90) REVERT: C 125 ASP cc_start: 0.7805 (m-30) cc_final: 0.7486 (m-30) REVERT: C 145 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7638 (tt0) REVERT: C 224 MET cc_start: 0.8422 (ttt) cc_final: 0.7995 (ttt) REVERT: C 235 MET cc_start: 0.9089 (mtp) cc_final: 0.8784 (mtt) REVERT: C 320 MET cc_start: 0.8816 (ptp) cc_final: 0.8467 (ptp) REVERT: E 69 MET cc_start: 0.8791 (mtp) cc_final: 0.8549 (mtp) REVERT: E 252 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: E 256 ASN cc_start: 0.8388 (t0) cc_final: 0.7993 (t0) REVERT: E 337 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8241 (mm) REVERT: E 471 LEU cc_start: 0.3307 (OUTLIER) cc_final: 0.3100 (tp) REVERT: e 30 GLU cc_start: 0.2728 (OUTLIER) cc_final: 0.2136 (tm-30) outliers start: 77 outliers final: 52 residues processed: 307 average time/residue: 0.7321 time to fit residues: 261.9106 Evaluate side-chains 295 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 231 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 468 GLU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 328 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 28 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 306 optimal weight: 6.9990 chunk 309 optimal weight: 4.9990 chunk 268 optimal weight: 0.3980 chunk 313 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 GLN D 372 HIS A 154 GLN A 226 HIS A 372 HIS F 154 GLN F 372 HIS B 154 GLN B 226 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.194387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.127212 restraints weight = 29472.133| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.83 r_work: 0.3019 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29658 Z= 0.102 Angle : 0.563 8.779 40176 Z= 0.283 Chirality : 0.045 0.157 4572 Planarity : 0.004 0.043 5106 Dihedral : 7.213 59.889 4053 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.82 % Favored : 93.78 % Rotamer: Outliers : 2.42 % Allowed : 21.53 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3588 helix: 1.50 (0.15), residues: 1254 sheet: -0.04 (0.23), residues: 540 loop : -1.48 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.008 0.001 TYR B 245 PHE 0.010 0.001 PHE D 225 TRP 0.007 0.001 TRP B 290 HIS 0.006 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (29646) covalent geometry : angle 0.56344 / 0.28 (40176) hydrogen bonds : bond 0.03274 / 2.15 ( 1032) hydrogen bonds : angle 4.32726 / 3.05 ( 2934) Misc. bond : bond 0.00016 / 0.01 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13896.07 seconds wall clock time: 236 minutes 55.64 seconds (14215.64 seconds total)